Multiple sequence alignment - TraesCS4D01G100600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G100600 chr4D 100.000 3851 0 0 1 3851 77909495 77905645 0.000000e+00 7112.0
1 TraesCS4D01G100600 chr4D 93.528 2534 94 27 1373 3851 77296786 77294268 0.000000e+00 3707.0
2 TraesCS4D01G100600 chr4D 89.077 650 36 14 530 1167 77297426 77296800 0.000000e+00 774.0
3 TraesCS4D01G100600 chr4D 83.529 510 47 18 1 502 196789631 196790111 3.530000e-120 442.0
4 TraesCS4D01G100600 chr4D 96.774 31 1 0 3021 3051 77295069 77295039 7.000000e-03 52.8
5 TraesCS4D01G100600 chr4B 93.635 2561 122 15 545 3080 109412063 109409519 0.000000e+00 3788.0
6 TraesCS4D01G100600 chr4B 88.757 507 48 6 3 502 427271469 427271973 2.540000e-171 612.0
7 TraesCS4D01G100600 chr4B 86.102 590 52 13 3053 3615 109409576 109408990 3.290000e-170 608.0
8 TraesCS4D01G100600 chr4B 84.646 508 44 16 1 502 480297704 480298183 3.480000e-130 475.0
9 TraesCS4D01G100600 chr1B 87.451 510 48 11 1 502 30648074 30647573 1.200000e-159 573.0
10 TraesCS4D01G100600 chr1B 87.059 510 50 11 1 502 30659488 30658987 2.600000e-156 562.0
11 TraesCS4D01G100600 chr4A 87.059 510 51 10 1 502 718230384 718230886 2.600000e-156 562.0
12 TraesCS4D01G100600 chr4A 78.661 478 76 21 2363 2826 665843364 665843829 1.050000e-75 294.0
13 TraesCS4D01G100600 chr3A 81.453 523 45 24 1 502 359349507 359349998 7.810000e-102 381.0
14 TraesCS4D01G100600 chr7D 81.548 504 53 15 1 493 625528888 625529362 2.810000e-101 379.0
15 TraesCS4D01G100600 chr7D 81.238 501 55 13 1 493 73567235 73566766 6.080000e-98 368.0
16 TraesCS4D01G100600 chr7A 80.159 504 62 13 1 493 688724923 688724447 3.680000e-90 342.0
17 TraesCS4D01G100600 chr1A 79.804 510 49 21 3 502 395456479 395456944 4.800000e-84 322.0
18 TraesCS4D01G100600 chr2B 82.573 241 29 7 267 497 541890730 541890967 2.350000e-47 200.0
19 TraesCS4D01G100600 chr6D 97.895 95 2 0 408 502 22657973 22657879 8.560000e-37 165.0
20 TraesCS4D01G100600 chr6D 97.895 95 2 0 408 502 22808945 22808851 8.560000e-37 165.0
21 TraesCS4D01G100600 chr6D 95.789 95 4 0 408 502 22353763 22353669 1.850000e-33 154.0
22 TraesCS4D01G100600 chr6D 95.789 95 4 0 408 502 22447711 22447617 1.850000e-33 154.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G100600 chr4D 77905645 77909495 3850 True 7112.000000 7112 100.000000 1 3851 1 chr4D.!!$R1 3850
1 TraesCS4D01G100600 chr4D 77294268 77297426 3158 True 1511.266667 3707 93.126333 530 3851 3 chr4D.!!$R2 3321
2 TraesCS4D01G100600 chr4B 109408990 109412063 3073 True 2198.000000 3788 89.868500 545 3615 2 chr4B.!!$R1 3070
3 TraesCS4D01G100600 chr4B 427271469 427271973 504 False 612.000000 612 88.757000 3 502 1 chr4B.!!$F1 499
4 TraesCS4D01G100600 chr1B 30647573 30648074 501 True 573.000000 573 87.451000 1 502 1 chr1B.!!$R1 501
5 TraesCS4D01G100600 chr1B 30658987 30659488 501 True 562.000000 562 87.059000 1 502 1 chr1B.!!$R2 501
6 TraesCS4D01G100600 chr4A 718230384 718230886 502 False 562.000000 562 87.059000 1 502 1 chr4A.!!$F2 501

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
539 553 0.038526 TCGCTCCTTTTCCTCGACAC 60.039 55.0 0.00 0.0 0.00 3.67 F
702 726 0.171903 CCCATTGCTCAAGCTTTCCG 59.828 55.0 0.00 0.0 42.66 4.30 F
869 908 0.457851 CTCCTCGGACACATCAGACC 59.542 60.0 0.00 0.0 0.00 3.85 F
2647 2707 0.401738 TTCCCAGGGACAAAGAGCTG 59.598 55.0 8.12 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 2327 0.890996 GAACCCCAGCTGGTGACAAG 60.891 60.000 30.63 14.33 42.06 3.16 R
2556 2616 0.885879 CAAGCCAGCAATTCTCTGCA 59.114 50.000 0.00 0.00 45.18 4.41 R
2667 2727 7.038729 ACAGAAGATCTCTCCATTGAACTGTAA 60.039 37.037 0.00 0.00 33.10 2.41 R
3713 3809 0.259065 ACGCCAGGGATGAGAGAGTA 59.741 55.000 0.00 0.00 0.00 2.59 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 4.499357 GCCTTGGTACTCCTACAATACTCG 60.499 50.000 0.00 0.00 34.23 4.18
79 80 6.850555 ACTCCTACAATACTCGTACAGTTTC 58.149 40.000 3.77 0.00 36.43 2.78
96 97 1.601419 TTCTCGAGGTTGCTACCCGG 61.601 60.000 21.00 11.92 46.28 5.73
123 124 4.199310 CACATTTACCAATCACCCTCGAT 58.801 43.478 0.00 0.00 0.00 3.59
135 136 5.432885 TCACCCTCGATCAAAAAGAAAAC 57.567 39.130 0.00 0.00 0.00 2.43
148 149 8.364129 TCAAAAAGAAAACTGGAATAATGCAC 57.636 30.769 0.00 0.00 0.00 4.57
168 169 9.638239 AATGCACATTTAAACATTTCTTACGAT 57.362 25.926 0.00 0.00 28.54 3.73
186 187 2.224378 CGATATGAGGCAACACCCATCT 60.224 50.000 0.00 0.00 40.58 2.90
239 242 6.899393 TGATTAATCAAGACAAGCAAACCT 57.101 33.333 15.82 0.00 33.08 3.50
271 274 6.438741 ACATGAACCTCTTTAGAGAGTCATCA 59.561 38.462 16.06 10.87 46.59 3.07
272 275 6.522625 TGAACCTCTTTAGAGAGTCATCAG 57.477 41.667 9.29 0.00 46.59 2.90
280 283 6.826231 TCTTTAGAGAGTCATCAGAAGATCGT 59.174 38.462 0.00 0.00 30.20 3.73
285 288 1.102978 TCATCAGAAGATCGTGCGGA 58.897 50.000 0.00 0.00 30.20 5.54
314 317 6.680874 AAGAGAGTCGTTATAAGATGACGT 57.319 37.500 0.00 0.00 42.12 4.34
315 318 6.680874 AGAGAGTCGTTATAAGATGACGTT 57.319 37.500 0.00 0.00 42.12 3.99
323 326 6.809689 TCGTTATAAGATGACGTTGAACACAT 59.190 34.615 5.04 5.04 42.12 3.21
371 374 9.067986 AGGAAGGAGTAATTCAACAGTAAAAAG 57.932 33.333 0.00 0.00 0.00 2.27
373 376 7.215719 AGGAGTAATTCAACAGTAAAAAGGC 57.784 36.000 0.00 0.00 0.00 4.35
374 377 6.208797 AGGAGTAATTCAACAGTAAAAAGGCC 59.791 38.462 0.00 0.00 0.00 5.19
378 388 1.868498 TCAACAGTAAAAAGGCCGTCG 59.132 47.619 0.00 0.00 0.00 5.12
396 406 2.989840 GTCGCCTGATGTATGTGATAGC 59.010 50.000 0.00 0.00 0.00 2.97
411 421 6.135290 TGTGATAGCCAAAAAGATATGTGC 57.865 37.500 0.00 0.00 0.00 4.57
416 426 7.720957 TGATAGCCAAAAAGATATGTGCTACAT 59.279 33.333 6.93 6.93 42.35 2.29
420 430 7.339212 AGCCAAAAAGATATGTGCTACATACAA 59.661 33.333 10.03 0.00 43.13 2.41
502 516 8.876303 TTGTGCAATAGAATATATAATGCCCA 57.124 30.769 0.00 0.00 29.68 5.36
503 517 8.279970 TGTGCAATAGAATATATAATGCCCAC 57.720 34.615 0.00 0.00 29.68 4.61
504 518 7.339212 TGTGCAATAGAATATATAATGCCCACC 59.661 37.037 0.00 0.00 29.68 4.61
505 519 6.542005 TGCAATAGAATATATAATGCCCACCG 59.458 38.462 5.79 0.00 29.68 4.94
506 520 6.765989 GCAATAGAATATATAATGCCCACCGA 59.234 38.462 0.00 0.00 0.00 4.69
507 521 7.282224 GCAATAGAATATATAATGCCCACCGAA 59.718 37.037 0.00 0.00 0.00 4.30
508 522 9.342308 CAATAGAATATATAATGCCCACCGAAT 57.658 33.333 0.00 0.00 0.00 3.34
509 523 9.561069 AATAGAATATATAATGCCCACCGAATC 57.439 33.333 0.00 0.00 0.00 2.52
510 524 6.357367 AGAATATATAATGCCCACCGAATCC 58.643 40.000 0.00 0.00 0.00 3.01
511 525 2.871096 TATAATGCCCACCGAATCCC 57.129 50.000 0.00 0.00 0.00 3.85
512 526 0.112412 ATAATGCCCACCGAATCCCC 59.888 55.000 0.00 0.00 0.00 4.81
513 527 1.282653 TAATGCCCACCGAATCCCCA 61.283 55.000 0.00 0.00 0.00 4.96
514 528 2.161713 AATGCCCACCGAATCCCCAA 62.162 55.000 0.00 0.00 0.00 4.12
515 529 2.440247 GCCCACCGAATCCCCAAG 60.440 66.667 0.00 0.00 0.00 3.61
516 530 3.087065 CCCACCGAATCCCCAAGT 58.913 61.111 0.00 0.00 0.00 3.16
517 531 1.077716 CCCACCGAATCCCCAAGTC 60.078 63.158 0.00 0.00 0.00 3.01
518 532 1.682849 CCACCGAATCCCCAAGTCA 59.317 57.895 0.00 0.00 0.00 3.41
519 533 0.676782 CCACCGAATCCCCAAGTCAC 60.677 60.000 0.00 0.00 0.00 3.67
520 534 0.324943 CACCGAATCCCCAAGTCACT 59.675 55.000 0.00 0.00 0.00 3.41
521 535 0.613777 ACCGAATCCCCAAGTCACTC 59.386 55.000 0.00 0.00 0.00 3.51
522 536 0.460284 CCGAATCCCCAAGTCACTCG 60.460 60.000 0.00 0.00 0.00 4.18
523 537 1.084370 CGAATCCCCAAGTCACTCGC 61.084 60.000 0.00 0.00 0.00 5.03
524 538 0.250513 GAATCCCCAAGTCACTCGCT 59.749 55.000 0.00 0.00 0.00 4.93
525 539 0.250513 AATCCCCAAGTCACTCGCTC 59.749 55.000 0.00 0.00 0.00 5.03
526 540 1.617947 ATCCCCAAGTCACTCGCTCC 61.618 60.000 0.00 0.00 0.00 4.70
527 541 2.286523 CCCCAAGTCACTCGCTCCT 61.287 63.158 0.00 0.00 0.00 3.69
528 542 1.674057 CCCAAGTCACTCGCTCCTT 59.326 57.895 0.00 0.00 0.00 3.36
534 548 1.273886 AGTCACTCGCTCCTTTTCCTC 59.726 52.381 0.00 0.00 0.00 3.71
539 553 0.038526 TCGCTCCTTTTCCTCGACAC 60.039 55.000 0.00 0.00 0.00 3.67
541 555 1.872237 CGCTCCTTTTCCTCGACACAA 60.872 52.381 0.00 0.00 0.00 3.33
548 562 2.971660 TTCCTCGACACAAGTCACAA 57.028 45.000 0.00 0.00 45.23 3.33
559 574 1.789464 CAAGTCACAAGTCACTCGCTC 59.211 52.381 0.00 0.00 0.00 5.03
605 620 6.462487 CGAATCCCCATAGCTGTAAGAGTAAA 60.462 42.308 0.00 0.00 34.07 2.01
630 646 4.038522 CCGCATCTATCTTCTCTCCTCAAA 59.961 45.833 0.00 0.00 0.00 2.69
631 647 5.279406 CCGCATCTATCTTCTCTCCTCAAAT 60.279 44.000 0.00 0.00 0.00 2.32
632 648 6.071672 CCGCATCTATCTTCTCTCCTCAAATA 60.072 42.308 0.00 0.00 0.00 1.40
670 694 5.047847 GCAAAATCAGCTCATGCATGTTAT 58.952 37.500 25.43 10.14 42.74 1.89
683 707 4.136796 TGCATGTTATGGCACTAGAATCC 58.863 43.478 0.00 0.00 34.58 3.01
702 726 0.171903 CCCATTGCTCAAGCTTTCCG 59.828 55.000 0.00 0.00 42.66 4.30
713 737 3.259876 TCAAGCTTTCCGTACATACCAGT 59.740 43.478 0.00 0.00 0.00 4.00
732 764 1.658596 GTATCGTTCGCATGCACTGAA 59.341 47.619 19.57 10.43 0.00 3.02
733 765 1.372582 ATCGTTCGCATGCACTGAAT 58.627 45.000 19.57 2.19 0.00 2.57
734 766 0.721154 TCGTTCGCATGCACTGAATC 59.279 50.000 19.57 7.26 0.00 2.52
735 767 0.723414 CGTTCGCATGCACTGAATCT 59.277 50.000 19.57 0.00 0.00 2.40
736 768 1.129251 CGTTCGCATGCACTGAATCTT 59.871 47.619 19.57 0.00 0.00 2.40
737 769 2.413239 CGTTCGCATGCACTGAATCTTT 60.413 45.455 19.57 0.00 0.00 2.52
738 770 2.905959 TCGCATGCACTGAATCTTTG 57.094 45.000 19.57 0.00 0.00 2.77
739 771 1.469703 TCGCATGCACTGAATCTTTGG 59.530 47.619 19.57 0.00 0.00 3.28
784 816 2.280183 GCGATCGAAGACACTGTTCATC 59.720 50.000 21.57 0.00 42.51 2.92
869 908 0.457851 CTCCTCGGACACATCAGACC 59.542 60.000 0.00 0.00 0.00 3.85
928 967 3.560105 CAATCTTTCTCTCCCCATTCCC 58.440 50.000 0.00 0.00 0.00 3.97
965 1004 1.362224 TTACCTGGCAGCTTCTTCCT 58.638 50.000 9.56 0.00 0.00 3.36
1170 1209 1.817941 CGGCAATAAGGGTCCGGTG 60.818 63.158 0.00 0.00 38.35 4.94
1180 1219 2.048127 GTCCGGTGTCTGTCCAGC 60.048 66.667 0.00 0.00 0.00 4.85
1195 1234 1.628340 TCCAGCTTCTCCGGAAATTCA 59.372 47.619 5.23 0.00 0.00 2.57
1244 1283 3.642901 CGGATCTAGACACCGTTGG 57.357 57.895 23.64 4.72 41.47 3.77
1249 1288 1.100510 TCTAGACACCGTTGGGATCG 58.899 55.000 0.00 0.00 36.97 3.69
1250 1289 1.100510 CTAGACACCGTTGGGATCGA 58.899 55.000 0.00 0.00 36.97 3.59
1297 1336 1.707989 TGCCCTTTGTGAACCTATGGA 59.292 47.619 0.00 0.00 0.00 3.41
1309 1348 2.919228 ACCTATGGATCCGTTTTGCTC 58.081 47.619 12.82 0.00 0.00 4.26
1336 1375 2.594962 AAAGTTCGTGCGCTCACCG 61.595 57.895 9.73 5.96 40.04 4.94
1338 1377 3.764049 GTTCGTGCGCTCACCGTC 61.764 66.667 9.73 1.09 40.04 4.79
1340 1379 4.700365 TCGTGCGCTCACCGTCTG 62.700 66.667 9.73 0.00 40.04 3.51
1350 1389 2.099921 GCTCACCGTCTGTCACTATGAT 59.900 50.000 0.00 0.00 0.00 2.45
1351 1390 3.700154 CTCACCGTCTGTCACTATGATG 58.300 50.000 0.00 0.00 0.00 3.07
1352 1391 3.352648 TCACCGTCTGTCACTATGATGA 58.647 45.455 0.00 0.00 0.00 2.92
1363 1402 6.648725 GTCACTATGATGACTGTAACCAAC 57.351 41.667 4.38 0.00 44.71 3.77
1397 1436 1.377856 GCCTGCCCTTTGTCTCTCC 60.378 63.158 0.00 0.00 0.00 3.71
1441 1480 2.154462 CTGGTGTTGGCTTACAAGGAG 58.846 52.381 0.00 0.00 40.38 3.69
1611 1650 2.103771 TGCTCCATGCCTTGTATCTCTC 59.896 50.000 0.00 0.00 42.00 3.20
1723 1762 6.644347 CACCTTACCTCACAAGATATCTGTT 58.356 40.000 5.86 0.00 0.00 3.16
1748 1787 3.795688 ATATAGCCAATCTGGGGTGTG 57.204 47.619 0.00 0.00 39.43 3.82
1805 1852 3.167921 TGCAAATAATGATGGCAGCAC 57.832 42.857 7.97 0.00 0.00 4.40
1868 1915 8.192774 GCATTTGGAGTTGATATCTTCATTTGA 58.807 33.333 3.98 0.00 33.34 2.69
2064 2111 7.432869 TGCAGTTTACTTTATGTTTCTGCAAT 58.567 30.769 12.86 0.00 43.98 3.56
2213 2260 9.802039 AGGAATTTATTAAACACTACCTGTTCA 57.198 29.630 0.00 0.00 42.70 3.18
2225 2272 5.696724 CACTACCTGTTCAAGAATCTTTCGT 59.303 40.000 0.00 0.00 34.02 3.85
2267 2327 8.840321 AGACAATAAACAGACATTATGTATGCC 58.160 33.333 18.38 0.00 42.86 4.40
2537 2597 5.723295 AGAGAAGCTCAGTCTTCATCTTTC 58.277 41.667 10.34 1.32 43.64 2.62
2639 2699 3.050089 TGTTTCTAGTTTCCCAGGGACA 58.950 45.455 8.12 0.00 0.00 4.02
2647 2707 0.401738 TTCCCAGGGACAAAGAGCTG 59.598 55.000 8.12 0.00 0.00 4.24
2667 2727 7.449704 AGAGCTGATGTTAAAATGAAAGGAAGT 59.550 33.333 0.00 0.00 0.00 3.01
2933 2998 2.161855 TGGAAACCATGCATGACACTC 58.838 47.619 28.31 16.69 0.00 3.51
2949 3014 3.636764 GACACTCTGTGGGGAACAAAAAT 59.363 43.478 2.72 0.00 38.67 1.82
2977 3042 1.272203 ACCCGGCATGTGGATTTGTTA 60.272 47.619 0.00 0.00 0.00 2.41
3141 3206 7.220875 GCTCTTTTTAGTAACATTAATGCCTGC 59.779 37.037 15.48 6.73 0.00 4.85
3192 3258 3.242739 ACGCAAATGTTGACTGTCTTGTC 60.243 43.478 9.51 1.50 37.47 3.18
3193 3259 3.242706 CGCAAATGTTGACTGTCTTGTCA 60.243 43.478 9.51 3.76 44.17 3.58
3220 3310 1.033574 GGTACTCATGGGAGACGAGG 58.966 60.000 0.00 0.00 44.26 4.63
3245 3336 3.178865 TCACTCCCCTCTTTACGGAATT 58.821 45.455 0.00 0.00 0.00 2.17
3410 3502 4.158394 AGGAACGCTGCACATTCATTAAAT 59.842 37.500 0.00 0.00 0.00 1.40
3417 3509 7.138081 CGCTGCACATTCATTAAATAATGGTA 58.862 34.615 12.02 3.33 42.46 3.25
3475 3567 6.500751 AGGGACAAGTCAGAAAATACCTTAGA 59.499 38.462 2.29 0.00 0.00 2.10
3551 3643 4.705023 CCCCTGTTTCGTTCCTTAATTCAT 59.295 41.667 0.00 0.00 0.00 2.57
3702 3798 4.252073 GCTGTCATGTCCATATCCATCTC 58.748 47.826 0.00 0.00 0.00 2.75
3713 3809 6.779539 GTCCATATCCATCTCCCTTCATTTTT 59.220 38.462 0.00 0.00 0.00 1.94
3720 3816 6.445139 TCCATCTCCCTTCATTTTTACTCTCT 59.555 38.462 0.00 0.00 0.00 3.10
3721 3817 6.765512 CCATCTCCCTTCATTTTTACTCTCTC 59.234 42.308 0.00 0.00 0.00 3.20
3722 3818 6.935240 TCTCCCTTCATTTTTACTCTCTCA 57.065 37.500 0.00 0.00 0.00 3.27
3730 3826 3.914426 TTTTACTCTCTCATCCCTGGC 57.086 47.619 0.00 0.00 0.00 4.85
3736 3832 2.821366 CTCATCCCTGGCGTGCAC 60.821 66.667 6.82 6.82 0.00 4.57
3795 3898 7.869800 TGCTTGTTTTGAAACTTTTTGATGTT 58.130 26.923 7.97 0.00 39.59 2.71
3816 3919 9.817809 GATGTTATGAGAAGAATACACAACCTA 57.182 33.333 0.00 0.00 0.00 3.08
3834 3937 8.393366 CACAACCTATGTATTCTTGTCATTGAG 58.607 37.037 0.00 0.00 41.46 3.02
3842 3945 8.032952 TGTATTCTTGTCATTGAGCAGTTTAG 57.967 34.615 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 2.500098 TGTAGGAGTACCAAGGCACATC 59.500 50.000 0.00 0.00 38.94 3.06
70 71 3.027974 AGCAACCTCGAGAAACTGTAC 57.972 47.619 15.71 0.00 0.00 2.90
79 80 1.033746 TACCGGGTAGCAACCTCGAG 61.034 60.000 6.32 5.13 45.95 4.04
84 85 0.108472 GTGTCTACCGGGTAGCAACC 60.108 60.000 26.14 14.98 45.97 3.77
96 97 5.497474 AGGGTGATTGGTAAATGTGTCTAC 58.503 41.667 0.00 0.00 0.00 2.59
123 124 7.984050 TGTGCATTATTCCAGTTTTCTTTTTGA 59.016 29.630 0.00 0.00 0.00 2.69
166 167 3.498774 AGATGGGTGTTGCCTCATATC 57.501 47.619 0.00 0.00 37.43 1.63
168 169 3.737559 AAAGATGGGTGTTGCCTCATA 57.262 42.857 0.00 0.00 37.43 2.15
205 208 8.578448 TGTCTTGATTAATCAAATGATGGACA 57.422 30.769 27.72 27.72 45.26 4.02
213 216 8.370182 AGGTTTGCTTGTCTTGATTAATCAAAT 58.630 29.630 26.57 0.00 45.26 2.32
216 219 6.489700 TGAGGTTTGCTTGTCTTGATTAATCA 59.510 34.615 14.23 14.23 34.44 2.57
220 223 4.216257 GCTGAGGTTTGCTTGTCTTGATTA 59.784 41.667 0.00 0.00 0.00 1.75
239 242 6.437477 TCTCTAAAGAGGTTCATGTTAGCTGA 59.563 38.462 7.14 0.00 42.30 4.26
271 274 1.464734 TCTCTTCCGCACGATCTTCT 58.535 50.000 0.00 0.00 0.00 2.85
272 275 2.279582 TTCTCTTCCGCACGATCTTC 57.720 50.000 0.00 0.00 0.00 2.87
280 283 1.200252 CGACTCTCTTTCTCTTCCGCA 59.800 52.381 0.00 0.00 0.00 5.69
285 288 9.179909 TCATCTTATAACGACTCTCTTTCTCTT 57.820 33.333 0.00 0.00 0.00 2.85
340 343 6.726764 ACTGTTGAATTACTCCTTCCTCTACT 59.273 38.462 0.00 0.00 0.00 2.57
343 346 7.554959 TTACTGTTGAATTACTCCTTCCTCT 57.445 36.000 0.00 0.00 0.00 3.69
356 359 3.058501 CGACGGCCTTTTTACTGTTGAAT 60.059 43.478 0.00 0.00 0.00 2.57
373 376 0.102300 TCACATACATCAGGCGACGG 59.898 55.000 0.00 0.00 0.00 4.79
374 377 2.140065 ATCACATACATCAGGCGACG 57.860 50.000 0.00 0.00 0.00 5.12
378 388 3.407424 TGGCTATCACATACATCAGGC 57.593 47.619 0.00 0.00 0.00 4.85
493 507 0.112412 GGGGATTCGGTGGGCATTAT 59.888 55.000 0.00 0.00 0.00 1.28
496 510 2.572333 CTTGGGGATTCGGTGGGCAT 62.572 60.000 0.00 0.00 0.00 4.40
502 516 0.613777 GAGTGACTTGGGGATTCGGT 59.386 55.000 0.00 0.00 0.00 4.69
503 517 0.460284 CGAGTGACTTGGGGATTCGG 60.460 60.000 0.00 0.00 0.00 4.30
504 518 1.084370 GCGAGTGACTTGGGGATTCG 61.084 60.000 1.41 0.00 0.00 3.34
505 519 0.250513 AGCGAGTGACTTGGGGATTC 59.749 55.000 1.41 0.00 0.00 2.52
506 520 0.250513 GAGCGAGTGACTTGGGGATT 59.749 55.000 1.41 0.00 0.00 3.01
507 521 1.617947 GGAGCGAGTGACTTGGGGAT 61.618 60.000 1.41 0.00 0.00 3.85
508 522 2.283529 GGAGCGAGTGACTTGGGGA 61.284 63.158 1.41 0.00 0.00 4.81
509 523 1.831652 AAGGAGCGAGTGACTTGGGG 61.832 60.000 1.41 0.00 0.00 4.96
510 524 0.035458 AAAGGAGCGAGTGACTTGGG 59.965 55.000 1.41 0.00 0.00 4.12
511 525 1.801178 GAAAAGGAGCGAGTGACTTGG 59.199 52.381 1.41 0.00 0.00 3.61
512 526 1.801178 GGAAAAGGAGCGAGTGACTTG 59.199 52.381 0.00 0.00 0.00 3.16
513 527 1.694696 AGGAAAAGGAGCGAGTGACTT 59.305 47.619 0.00 0.00 0.00 3.01
514 528 1.273886 GAGGAAAAGGAGCGAGTGACT 59.726 52.381 0.00 0.00 0.00 3.41
515 529 1.715993 GAGGAAAAGGAGCGAGTGAC 58.284 55.000 0.00 0.00 0.00 3.67
516 530 0.243907 CGAGGAAAAGGAGCGAGTGA 59.756 55.000 0.00 0.00 0.00 3.41
517 531 0.243907 TCGAGGAAAAGGAGCGAGTG 59.756 55.000 0.00 0.00 0.00 3.51
518 532 0.244178 GTCGAGGAAAAGGAGCGAGT 59.756 55.000 0.00 0.00 0.00 4.18
519 533 0.243907 TGTCGAGGAAAAGGAGCGAG 59.756 55.000 0.00 0.00 0.00 5.03
520 534 0.038526 GTGTCGAGGAAAAGGAGCGA 60.039 55.000 0.00 0.00 0.00 4.93
521 535 0.319555 TGTGTCGAGGAAAAGGAGCG 60.320 55.000 0.00 0.00 0.00 5.03
522 536 1.801178 CTTGTGTCGAGGAAAAGGAGC 59.199 52.381 0.00 0.00 0.00 4.70
523 537 3.060602 GACTTGTGTCGAGGAAAAGGAG 58.939 50.000 0.00 0.00 33.15 3.69
524 538 2.432874 TGACTTGTGTCGAGGAAAAGGA 59.567 45.455 0.00 0.00 45.70 3.36
525 539 2.544267 GTGACTTGTGTCGAGGAAAAGG 59.456 50.000 0.00 0.00 45.70 3.11
526 540 3.194861 TGTGACTTGTGTCGAGGAAAAG 58.805 45.455 0.00 0.00 45.70 2.27
527 541 3.254470 TGTGACTTGTGTCGAGGAAAA 57.746 42.857 0.00 0.00 45.70 2.29
528 542 2.971660 TGTGACTTGTGTCGAGGAAA 57.028 45.000 0.00 0.00 45.70 3.13
534 548 2.535984 GAGTGACTTGTGACTTGTGTCG 59.464 50.000 0.00 0.00 45.70 4.35
539 553 1.789464 GAGCGAGTGACTTGTGACTTG 59.211 52.381 1.20 3.71 0.00 3.16
541 555 0.315568 GGAGCGAGTGACTTGTGACT 59.684 55.000 1.20 0.00 0.00 3.41
548 562 0.393808 GGAGAGAGGAGCGAGTGACT 60.394 60.000 0.00 0.00 0.00 3.41
559 574 2.202676 GAGCGTTGCGGAGAGAGG 60.203 66.667 0.00 0.00 0.00 3.69
605 620 3.571590 AGGAGAGAAGATAGATGCGGTT 58.428 45.455 0.00 0.00 0.00 4.44
630 646 5.545658 TTTTGCGCTCTCGAGAAAAATAT 57.454 34.783 17.36 0.00 38.10 1.28
631 647 5.121611 TGATTTTGCGCTCTCGAGAAAAATA 59.878 36.000 24.87 15.50 36.17 1.40
632 648 3.896648 TTTTGCGCTCTCGAGAAAAAT 57.103 38.095 17.36 0.00 38.10 1.82
670 694 1.410083 GCAATGGGGATTCTAGTGCCA 60.410 52.381 0.00 0.00 0.00 4.92
683 707 0.171903 CGGAAAGCTTGAGCAATGGG 59.828 55.000 0.00 0.00 45.16 4.00
702 726 3.956233 TGCGAACGATACTGGTATGTAC 58.044 45.455 0.00 0.00 0.00 2.90
713 737 2.003196 TTCAGTGCATGCGAACGATA 57.997 45.000 14.09 0.00 0.00 2.92
732 764 6.045577 TCTCCCCTCTAAGAAAAACCAAAGAT 59.954 38.462 0.00 0.00 0.00 2.40
733 765 5.371472 TCTCCCCTCTAAGAAAAACCAAAGA 59.629 40.000 0.00 0.00 0.00 2.52
734 766 5.631119 TCTCCCCTCTAAGAAAAACCAAAG 58.369 41.667 0.00 0.00 0.00 2.77
735 767 5.656549 TCTCCCCTCTAAGAAAAACCAAA 57.343 39.130 0.00 0.00 0.00 3.28
736 768 5.631119 CTTCTCCCCTCTAAGAAAAACCAA 58.369 41.667 0.00 0.00 31.45 3.67
737 769 4.506802 GCTTCTCCCCTCTAAGAAAAACCA 60.507 45.833 0.00 0.00 31.45 3.67
738 770 4.011023 GCTTCTCCCCTCTAAGAAAAACC 58.989 47.826 0.00 0.00 31.45 3.27
739 771 3.685272 CGCTTCTCCCCTCTAAGAAAAAC 59.315 47.826 0.00 0.00 31.45 2.43
891 930 2.085343 ATTGGCTCACCTGGTTGCCT 62.085 55.000 29.28 15.52 45.11 4.75
895 934 2.108952 AGAAAGATTGGCTCACCTGGTT 59.891 45.455 0.00 0.00 36.63 3.67
935 974 0.596082 GCCAGGTAAAGCAGCGAAAA 59.404 50.000 0.00 0.00 0.00 2.29
1170 1209 1.216710 CCGGAGAAGCTGGACAGAC 59.783 63.158 0.00 0.00 46.81 3.51
1180 1219 2.945668 GGTCCATGAATTTCCGGAGAAG 59.054 50.000 3.34 0.00 32.35 2.85
1230 1269 1.100510 CGATCCCAACGGTGTCTAGA 58.899 55.000 0.00 0.00 0.00 2.43
1244 1283 5.064707 TCACGGAATTTTCTGAATTCGATCC 59.935 40.000 6.15 4.74 37.48 3.36
1249 1288 5.790495 CGTCTTCACGGAATTTTCTGAATTC 59.210 40.000 6.15 0.00 42.73 2.17
1250 1289 5.468746 TCGTCTTCACGGAATTTTCTGAATT 59.531 36.000 6.15 0.00 46.70 2.17
1297 1336 1.446907 CTCTGCAGAGCAAAACGGAT 58.553 50.000 29.79 0.00 38.41 4.18
1309 1348 0.385223 GCACGAACTTTGCTCTGCAG 60.385 55.000 7.63 7.63 40.61 4.41
1340 1379 5.581085 GGTTGGTTACAGTCATCATAGTGAC 59.419 44.000 0.00 0.00 46.90 3.67
1350 1389 3.949113 GGTTGAAAGGTTGGTTACAGTCA 59.051 43.478 0.00 0.00 0.00 3.41
1351 1390 4.204799 AGGTTGAAAGGTTGGTTACAGTC 58.795 43.478 0.00 0.00 0.00 3.51
1352 1391 4.245251 AGGTTGAAAGGTTGGTTACAGT 57.755 40.909 0.00 0.00 0.00 3.55
1353 1392 5.617252 TCTAGGTTGAAAGGTTGGTTACAG 58.383 41.667 0.00 0.00 0.00 2.74
1354 1393 5.633655 TCTAGGTTGAAAGGTTGGTTACA 57.366 39.130 0.00 0.00 0.00 2.41
1361 1400 2.649816 AGGCCATCTAGGTTGAAAGGTT 59.350 45.455 5.01 0.00 40.61 3.50
1363 1402 2.648059 CAGGCCATCTAGGTTGAAAGG 58.352 52.381 5.01 0.00 40.61 3.11
1441 1480 5.331098 GCAGCTAGAAAAATCAAGAAGAGC 58.669 41.667 0.00 0.00 0.00 4.09
1611 1650 4.343814 ACACCTGAAAACCCCAATAGTTTG 59.656 41.667 0.00 0.00 37.50 2.93
1723 1762 5.610982 ACACCCCAGATTGGCTATATTTCTA 59.389 40.000 0.00 0.00 35.79 2.10
1805 1852 2.858260 GCACCGAGAACCACACAATTTG 60.858 50.000 0.00 0.00 0.00 2.32
2085 2132 4.393062 ACATCAAATCTTGCACTCCTAACG 59.607 41.667 0.00 0.00 0.00 3.18
2086 2133 5.886960 ACATCAAATCTTGCACTCCTAAC 57.113 39.130 0.00 0.00 0.00 2.34
2267 2327 0.890996 GAACCCCAGCTGGTGACAAG 60.891 60.000 30.63 14.33 42.06 3.16
2556 2616 0.885879 CAAGCCAGCAATTCTCTGCA 59.114 50.000 0.00 0.00 45.18 4.41
2639 2699 8.181904 TCCTTTCATTTTAACATCAGCTCTTT 57.818 30.769 0.00 0.00 0.00 2.52
2667 2727 7.038729 ACAGAAGATCTCTCCATTGAACTGTAA 60.039 37.037 0.00 0.00 33.10 2.41
2890 2953 7.505585 TCCATGTCTTAGAAAATTTGGTGTTCT 59.494 33.333 0.00 0.00 35.77 3.01
2933 2998 4.935352 TCTTCATTTTTGTTCCCCACAG 57.065 40.909 0.00 0.00 36.48 3.66
2949 3014 0.888736 CACATGCCGGGTGTTCTTCA 60.889 55.000 2.18 0.00 0.00 3.02
3086 3151 4.877282 AGAAGCCAGCGATCTTATTACTC 58.123 43.478 0.00 0.00 0.00 2.59
3192 3258 2.093181 TCCCATGAGTACCGACCATTTG 60.093 50.000 0.00 0.00 0.00 2.32
3193 3259 2.170607 CTCCCATGAGTACCGACCATTT 59.829 50.000 0.00 0.00 33.70 2.32
3220 3310 3.072211 CCGTAAAGAGGGGAGTGAAAAC 58.928 50.000 0.00 0.00 0.00 2.43
3245 3336 3.131577 ACTGAACAACTGAACGGTAGACA 59.868 43.478 0.00 0.00 0.00 3.41
3502 3594 6.992715 GTGGCCAGTTATAGTGAATCTGTAAT 59.007 38.462 5.11 0.00 33.57 1.89
3551 3643 8.839310 TGTCAAAAGAATTTCACAAAGGAAAA 57.161 26.923 0.00 0.00 37.28 2.29
3702 3798 5.825151 GGGATGAGAGAGTAAAAATGAAGGG 59.175 44.000 0.00 0.00 0.00 3.95
3713 3809 0.259065 ACGCCAGGGATGAGAGAGTA 59.741 55.000 0.00 0.00 0.00 2.59
3720 3816 4.758251 CGTGCACGCCAGGGATGA 62.758 66.667 28.16 0.00 0.00 2.92
3736 3832 4.853196 CAGAAAATAACCAATGAGCACACG 59.147 41.667 0.00 0.00 0.00 4.49
3813 3916 6.765036 ACTGCTCAATGACAAGAATACATAGG 59.235 38.462 0.00 0.00 0.00 2.57
3816 3919 7.458409 AAACTGCTCAATGACAAGAATACAT 57.542 32.000 0.00 0.00 0.00 2.29


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.